Limosilactobacillus fermentum in the theoretical composition was changed to Lactobacillus fermentum
## Error in dimnames(x) <- dn :
## length of 'dimnames' [1] not equal to array extent
These are the taxa that were found in the experimental data
## species taxid superkingdom phylum
## 1 Bacillus subtilis 1423 Bacteria Firmicutes
## 2 Enterococcus faecalis 1351 Bacteria Firmicutes
## 3 Escherichia coli 562 Bacteria Proteobacteria
## 4 Limosilactobacillus fermentum 1613 Bacteria Firmicutes
## 5 Listeria monocytogenes 1639 Bacteria Firmicutes
## 6 Pseudomonas aeruginosa 287 Bacteria Proteobacteria
## 7 Salmonella enterica 28901 Bacteria Proteobacteria
## 8 Staphylococcus aureus 1280 Bacteria Firmicutes
## class order family genus
## 1 Bacilli Bacillales Bacillaceae Bacillus
## 2 Bacilli Lactobacillales Enterococcaceae Enterococcus
## 3 Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia
## 4 Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus
## 5 Bacilli Bacillales Listeriaceae Listeria
## 6 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
## 7 Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella
## 8 Bacilli Bacillales Staphylococcaceae Staphylococcus
## count Gram Stain EXP_sum
## 1 1740000 + 2199.0567
## 2 990000 + 936.2883
## 3 1010000 - 1747.5300
## 4 1840000 + 1107.1917
## 5 1410000 + 869.5224
## 6 420000 - 109.1338
## 7 1040000 - 533.2867
## 8 1550000 + 945.2043
## is.significant N
## <lgcl> <int>
## 1: TRUE 2
## 2: FALSE 19
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.13738 0.36771 1.7447 0.222
## Residual 6 0.23623 0.63229
## Total 8 0.37361 1.00000
## is.significant N
## <lgcl> <int>
## 1: TRUE 8
## 2: FALSE 64
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.13798 0.36839 1.7498 0.21
## Residual 6 0.23656 0.63161
## Total 8 0.37454 1.00000
## is.significant N
## <lgcl> <int>
## 1: TRUE 27
## 2: FALSE 384
## 3: NA 12
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.13921 0.36991 1.7612 0.227
## Residual 6 0.23713 0.63009
## Total 8 0.37634 1.00000
## is.significant N
## <lgcl> <int>
## 1: TRUE 64
## 2: FALSE 721
## 3: NA 10
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.13985 0.37072 1.7674 0.215
## Residual 6 0.23739 0.62928
## Total 8 0.37724 1.00000